The X Files Phantoms
by hammy ham ham
Summary: The infamous FBI duo have set out for Amity Park to research Danny Phantom. Things start happening. A billionaire with an amnesia stricken daughter, a teenager with a grave secret to hide, a genetic mishap? Have they bitten off more than they can chew?
1. Prologue

This is an X-Files Danny Phantom crossover. Yes, that is creepy. Yes, I have no idea why nobody thought of it aside from a few aspiring Devianartists. Oh well.

This will be done in the style of a real X-Files episode. As in- little-to-none thoughts will be said, and nothing will stick out directly. However, for the sake of the story, some thought-attuned comments will be made. Also, despite my efforts, some MSR and DS have sneaked into this. If you don't support either... It could be ignored and thrown off as friendship, I guess, but it will be awkward.

This is going to be in an early-middle season, because I haven't seen the plot based episodes for the later seasons, but I don't want the pure skepticism Dana has in the early seasons, or the angst-ridden Mulder either.

XXX

FBI Headquarters, WASHINGTON D.C.

3:00 PM

Mulder was sitting at his desk, looking over a heavily worn black and white photograph of a blur in the night sky, a heavy crease covering the gray smudge of sky to the right of the mysterious smear. His chocolate eyes didn't move, didn't blink- just staring a hole into the old picture, the headline reading 'FLYING DISK SEEN OVER TEXAS CORN FIELD.'

The door to his office was clicked open, breaking the silence like a gun shot. Of sorts. For the first time in what could have been hours, he removed his eyes from the image long enough to turn and get a good look at the doorway. A look of childish curiosity covered his face as the door opened to reveal his partner in crime, Dana Scully.

The astute redhead walked carefully through the mingled assortment of garbage decorating the storage-closet-turned-office, before making out the haphazard attempt at a path through the various this and that.

Once the obscure spit of exposed rug had been traversed, she stood next to his desk while holding a rather thin file and a mischievous, teasing look, like the cat that caught the fattest rat in the house.

"Mulder, I have a case I have an inkling you won't pass up. I've decided to at least _try _to meet you halfway on this whole paranormal business." she teased while fingering the corner of the file's cover, her face holding an emotion rarely seen on the pathologist- mischief. Mischief setting Mulder on edge.

He barely had to take a look at his smirking partner before immediately deciding that whatever this was had to be trouble of some subspecies. He raised an eyebrow at the seldom- seen curve of her lips, his mind whirring and stirring with ideas of what could have driven his normally serious-as-a-heart-attack friend into such an unusual, almost _childish_ state.

He continued to gaze into her deep blue eyes as he slowly took the file from her hands. His digits toyed with the corners where her fingers had, flicking the corner into a bend before opening the file to the front page, which he read swiftly. In neat, clean font were the words,

**-AMITY PARK CASE-**

**-OCTOBER 16TH, 2006-**

**-CLASSIFICATION: X FILE-**

**-AGENTS: MULDER, SCULLY-**

**-REGARDING: UNEXPLAINED SPECTRAL ACTIVITY-**

Mulder's eyebrow raise Northward at the title, thoughts stopping short at the word 'spectral'. He did a double take at the thin script before shaking his head. He looked at Scully incredulously, deadpanning, "Unexplained spectral activity? You mean ghost trouble? I thought we had an agreement against ghosts after that madhouse where we nearly shot each other full of hot lead on Christmas eve. Unless you forgot finding our own corpses under some floor boards?"

Scully shook her head at her partner, half-snorting amusedly at his remark. Only Mulder could make a comment like, and after how many years of tracking aliens? The one time she brings up something strange of her own and he discounts it immediately. Only for Mulder...

She shook her head at the fine example of hypocrisy spewed from the mouth of the man before her, muttering under her breath about Spooky not beginning to describe. She sighed and drew in a breath before responding, "As useless as it is for me to tell you it, this _is_ serious Mulder, they need our help. I thought you of all people would understand looking for help when you don't understand something."

Mulder's deadpan died in his mouth at that, and no response was given. Scully didn't miss the far away look that had suddenly sprung in his eyes, however, and immediately regretted the remark. She should know how sensitive it was to him... Hell, it was sensitive to _her_. Of all the below the belt comments she could have madr...

She inwardly sighed as her partner's features stuck. If she didn't so something, he might go back into one of his twenty-four hour depression. One of the last things he needed, either of them needed. She lifted one finger to poke him in the shoulder, resulting in a yelp and severe jerking before he realized it was just her finger.

"You gonna be okay? I could do this one on my own..." she chanced, although she knew it was probably a bad move.

Mulder blinked once, twice before offering a smile he could only hope looked halfway real. "After you nearly died from some insane villagers putting some parasite into your back? Scully, I can't leave you alone anywhere. Continue- just, be more careful, alright?"

She just nodded, unsure whether to smile or cry at the pain in his voice. He was trying to joke, she knew it- but that didn't help. She continue3d on, hoping things would resolve themselves, for once.

"Amity Park, California has experienced paranormal activity far more often than any other city in the United States. Not only are ghosts seen often, they have actually caused damage in the town. Physical damage, to property mostly."

Mulder's mouth, once again capable of motion after the dead set of thought, was beginning to hang lower and lower with each word and syllable. He was left gaping at the end, his jaw staying several inches away from his upper lip for several moments before shaking himself and asking, "You mean these ghosts have actually interacted with the townsfolk? As in, ghost attacks?"

Scully took a deep breath and rolled her eyes, suppressing the urge to retort, 'is there an echo in here' at her partner, for his sake. She let the breath out slowly and sucked air back in, in the manner one would before explaining to a child. She waited for once tense moment before replying, "Not only once, but as often as three times in any given week. The activity began during Mid-September of last year. Also, it began incredibly suddenly. Prior to that point, there had been no reports of paranormal activity outside of the typical teenage pranks and campfire tales from the local boy scouts."

Mulder soaked this information in, raising his finger to the corner of his mouth. A question cropped up in his mind, one needed answering. In regard to its plea for release he separated his lips, breathing out, "So, what was so special about last September? It seems a little odd that anyone, even spirits, would suddenly spring out of nowhere in a town so small even _I _haven't heard of it. Think the Ghost Busters are listed under 'public service' or 'specialist' in the phone book?"

Scully suppressed a groan at the atrocious pun that had just flitted into her ears. She forced a grotesquely false grin, replying, "That's we're trying to find out. The first part. Fortunately- or not, depending on who you are- the attacks have centered around one ghost in particular. This ghost has claimed innocence, and the town was saved by this being in a city wide raid by an entity calling himself Pariah Dark, mythologically, the king of the undead.

"However, said ghost has cost millions in property damage during fights with other specters. There was also a hostage situation involving the mayor that the ghost has repeatedly claimed to be a frame up, although no proof has ever been brought forward on either side."

Mulder nodded, absorbing the information. "So, what do they want us to do with all of this? Usually they'll want us to solve a murder or a disappearance, but this, what are they asking for? They know the issue already. What's there for us to find out?" he pondered, gazing at Scully's stern, piercing eyes.

"They want us to find out why this ghost is around and the connections it has to the ghost attacks. Our ride is already set and accommodations made for however long we need to scope this _thing_ out. We have a lot to do and not much to go on aside from visual reports, and then even those have had several discrepancies involving his whether he has legs or a 'mist like tail' and the logo on his chest, most notably a teenage boy claiming that, when weakened by a shrinking device of some sort, the ghost's outfit changed from what can best be described as a jumpsuit into casual attire, as well as the darkening of hair color. Of course, the inclusion of a 'shrink device' certainly adds to his credibility..."

She could see that Mulder was trying, hard, on deciding if he should laugh or take the boy seriously. Admittedly, she was ready to sign the boy's loony bin papers... but that wasn't exactly her area of conduct.

"Fortunately, one piece of information is known-- a name has been given by figure itself." she said casually, although she could the sudden shine that came to her partner's eyes.

He, for whatever reason, loved giving little nicknames to animals they were dealing with. The fact that the specter might have done the same to himself... Well, it was rather like finding out that your favorite celebrity had the same flavor of ice cream, she supposed.

Both of Mulder's eyebrows were now so high they were nearly invisible in his chestnut hair. His mouth was open slightly. He ventured, "Oh? What has this entity named itself?"

Scully flipped the folder to a picture of a white haired, green eyed ghost in a black and silver jumpsuit floating high over a city, hands shining a bright green and body glowing faintly. "Danny Phantom."

------

This is a SUCKY first chapter... but bare with me, alright? This is only the prologue, anyway.


	2. Clouded Visions

So sorry about the time! There is no real excuse... But, I can contribute it partly to my muses. Not that they're not active- they're OVER active, and I can only do so many things at once while pleasing them.

They have been waging war in my head, literally. There are times when I can't even sleep for hours at a time because of the headache they're giving me. For every sentence I write, it takes a good couple of minutes before they can agree on how it should be phrased and such. The fact that they're polar opposites does not help. Four muses, one story... Got to love 'em...

East of Amity Park, California

7:00 AM Pacific Time

Mulder and Scully were nearing there final destination-- Amity International Airport. They were descending, nearing seventeen thousand feet, after four horrific hours of cramped quarters and stale, salty snacks. Their dietitians would have it in for them.

Scully was reading a book labeled 'Contact' with a passion in her center seat. She was determined to bridge the gap between her and Mulder over the paranormal, or else. She may have accepted it, even defended it, but she wanted to do more than that.

If she didn't, the gap would only grow, and the trust they had might fall through the fissure, no matter how stable the bridge. Mulder wasn't getting more logical, so she had to be more superstitious.

Said Mulder was, by gum, laughing all the while she was pondering this, happily answering the plane's trivia game with the enthusiasm anybody else would think only a child could muster. but Scully knew it was normal- it was Mulder in one of his many forms; the overenthusiastic child, amused by everything, no matter how absurd or naive.

He saw the next question come up, and grinned a feral grin behind his cup of complementary 'coffee' (if the standards allowed as such). He poked Scully in the shoulder playfully, grinning like a hyperactive nut. Or a kid that wants something from their mom and is ready to butter them up. Scully lowered her book to give him an incredulous stare, subconsciously raising her 'cutesy' shield. Big brown puppy dog eyes be damned, she was actually enjoying this story.

Mulder took no notice of his partner's less than enthusiastic reply to his continued prodding, and whispered in her ear, "Hey Scully; Do you know where was Elvis born?"

Sculled rolled her eyes at what she should have expected from her work partner. He'd never change. She silently berated herself for not seeing _that_ coming before answering, "Mulder, how should I know? I'm not exactly a rocker. Or a hipster. Or a rapper. Or much anything else besides Classical music; and maybe The Beatles when I feel like letting my hair down."

Mulder gawked at his partner's musical choice so long that the trivia game moved on to the next question, 'Who wrote Uncle Tom's Cabin?' "Come on Scully, not even you could be manage to be that high brow and still willingly come within a thirty mile radius of me. I know you have to have _something_ stashed on your walk man"

Scully rolled her eyes and returned to her book, murmuring, "Mulder, I don't even _have _a walk man..." However, her Carl Sagan novel was cut short by the sound of explosions echoing from somewhere far away.

Nowhere on the plane, at least- that was the farthest they could tell, as the thick skin of the plane would have distorted it. but it was a sound they had long trained their ears to pick up, no matter the distance or location.

Both the agents looked to each other, shrugged, and turned to look out Mulder's window, trying to see just what was going on in the open sky outside their compartment.

Suddenly, a black and white something, followed by a red something, darted from the right side of the window to the left, made a sharp turn, and raced toward the aircraft at a blinding pace. Calls of 'I'LL GET YOU GHOST!' were _just _audible through the thick glass making up the pane.

The white and black blur was growing bigger, eventually growing large enough to be recognized as a kind of humanoid figure. Of course, by the time that was apparent it was accelerating at an outrageous rate, and looked to be liable to crash into the plane. Quite hard.

Both agents let instinct take hold- they sheltered their head with their arms and watched out the corners of their eyes for the impact. An impact that would never come- the figure disappeared less than a second away from splattering like a bug on a windshield. It disappeared part way, anyway. There was still a sort of outline, like when two microscope slides aren't lined up just so.

The outline zoomed into the airplane, and then _through _it, right over the legs of our duo. Their drinks splattered all over their laps- not that they noticed in the excitement. Human figures flying through airplane walls tends to be a bit more attention grabbing than spilled water and diluted coffee.

Blasts were sounding from above now, along with cries of, "What're you thinking, you could've made me hit the plane!" which were followed by calls of, "_I'd _make _you _hit the plane? _You're_ the one with the gun!"

People all through the plane were beginning to notice what was going on and, as their instincts told them, started to panic. Someone behind the agents was chanting 'remember nine-eleven' under their breath while fingering their pocket. The agents were preparing to address the cabin when the intercom came on, diverting their attention from the flying figures.

_'Attention passengers- there is no cause for alarm. You have just been witness to one of the mysterious aerial battles between Danny Phantom and the Red Huntress, renowned through out the paranormal world! _

_'They have both moved away from the airspace. Stay calm, we will be landing shortly. Fasten your seat belts and return your seats to the up-right position"_

Both agents just sat there, stunned at the calm that took hold, as if two flying things hadn't just tried to kill each other over their heads. They stayed that until Mulder deadpanned, "There goes my kids-in-bed sheets theory."

They both watched across the aisle as the two forms shrank toward the horizon, occasional pink or green lights able to be seen even after they'd shrunk beyond recognition. They stared until the two were lost all together by the low cloud layer billowing around the plane.

Casper High School, Amity Park, California

11:00 AM

A thin blue eyed youth with messy black hair was sitting uncomfortably in his plastic desk-chair, fidgeting occasionally. He barely blinked, eying the clock with the kind of heated glare that didn't belong on someone twice his age. With every little tick, he tapped his index finger against the corner of the desk, bumping the calloused end into the same dented spot. "_Come on..."_

It rang, _at last_, in his opinion. He nearly jumped out of his seat, before the others had even reacted. In a burst of speed he grabbed his books, stuffed them into his heavily taped backpack, and made his way toward the door with more urgency than was absolutely necessary.

The others followed in single file, not bothering to pay attention to his odd behavior any more than to the pattern of the partly-cloudy sky. Neither had much outcome on their lives, and should not be treated as such. Such were normal, average.

On his way out the door, he stopped mid step, halting the students behind him. The others grumbled at the hold up, but made no words against the young man. His mouth opened in a look of utmost horror as he gasped openly at the empty hall. His breath was, oddly, a visible cloud of fog, despite the glowing sunlight beaming through the window and against his back.

He hastened his steps out of the room and almost ran into the closest restroom, dodging around the other students with a surprising ease. He slammed the heavy door behind himself and waited a minute to see if another would come. He checked under the stall doors for shoes or backpacks. They were empty- He was alone. He breathed out a sigh of relief, his breath no longer visible to the naked eye. He returned to the center of the small room, dropping everything off his back.

A bright light erupted from underneath the door of the restroom, and then disappeared just as suddenly, leaving those in the hallway to ponder at the unknown source. But none checked the room for problems- the light bulbs had been on the fritz in the bathrooms ever since school started, it was nothing unusual.

Although the boy's teacher would be left wondering where had had gone when his previous class was four doors down.


	3. Gauntlet

I'm not gonna sugar coat it- I'm starting to lose interest in Danny Phantom. No, not starting, I nearly have completely. I am, however, now a raving X-Phile, so maybe that'll kick up the old spirit to finish this thing. Maybe. Hopefully.

------

In the school parking lot, something akin to a mirage appeared, quick as a flash. After a moment, it became visible- the ghost from Scully's pictures in all his undead, glowing glory. He shook his hair about in the same manner as a wet dog would, bits of tar and dirt slipping falling like a cloud to the asphalt.

He growled as a bit fell in his eye, stinging slightly. He rubbed it agitatedly, hissing under his breath as it moved out from under the stubborn lid. The annoying bit of grit gone, he looked around the structure and trees, glaring at whatever he happened to be looking at as he inspected it. He grunted as his eyes closed, shaking his head and groaning.

"Nothing."

In complete disregard of his dead (and breathless) persona, a large gasp of mist came from his mouth, dissipating in the growing morning heat. He groaned under before he turned back to face the school, a disgruntled scowl on his face as he squinted into the bright sunlight, waiting for a cloud to soften the blast. He held his hand over his eyes, locking on to a ghoulish glow somewhere far off, behind the school.

His body became semi transparent again, like it did before hitting the plane and when he came out of the parking lot, and he darted next to the school, through trees and windowsills and anything else hanging from it. He disappeared as he passed windows, his invisibility hiding him from any scrutinizing eyes. He remained invisible all across the building, until reappearing on the other side of the school, as of yet undetected.

In front of him was the cause of the disturbance- an unnaturally large green eagle glowing like something out of a B grade horror movie, flying close to the ground and swiping at the empty air every now and again. He frowned as the huge eagle shredded apart a paper airplane that had flown through one of the school's windows. He flew around behind it, or at least, as best he could with it still circling like a buzzard. He threw his fist forward and shot a glowing green laser out of his knuckles at the eagle, causing it to shriek and be thrown back from its flight path.

Somewhere far below the battle, our two FBI agents had been driving when the sound of sizzling air and the awkward squawk of an injured animal drew their attention from the search for a certain 'Poe Avenue'. Scully gave her partner a deer-in-headlights look when she registered it wasn't the car'ds engine. He nodded slightly; he heard it too. "We may not have to look far for ghost activity after all" he said as he turned the car to the shoulder of the road, near the entrance to the High School.

The two were out of the car in a flash, looking for the source of the commotion. Finding it wasn't exactly hard, considering one was for the most part firing off explosions at the other. Mulder watched in silent awe of the two combatants, while Scully grimaced at seeing what looked like a corpse ready for the autopsy table flying around in mid air, almost like a normal, every day person. It was one thing to cut them up, but to see one moving around was _not_ something she was used to, even _with_ being around Mulder and working his kooky cases. It wasn't until a shot deflected by the eagle nearly beheaded them that they remembered that this was more than a fancy show.

"Don't let him out of your sight!" Mulder commanded as he grabbed his gun out of its holster and leveled it with Danny Phantom, Scully doing the same. He and Scully separated to watch the dog fight from opposite directions, and get him from whichever direction he went. They watched silently as the battle waged on, occasionally nodding or gesturing where the better cover would be.

The more humanoid ghost punched the eagle in the beak, causing the raptor to fall back with a pained squawk, glowing feathers flying from its badly singed wings. He flew up to intercept the bird mid arc, but was caught by a swipe of talons from the flying beast.

He yelped as the claws raked his limb, groping for where he was hit below his shoulder. Green blood flowed freely between his fingers and to the ground below, where it pooled in the crater formed from where one of his blasts missed it's mark.

He glared at the glowing avian before firing off a barrage of the glowing green blasts, assailing it and sending it crashing to the ground in a smoking mound of feathers. He reached behind his back and pulled out a silver and green cylinder, aiming it at the unconscious bird. He opened the top of the canister, and a dazzling blue and white light channeled outward, ensnaring the eagle. The bird gave out a squack as its body began changing shape, turning in a shape like pulled taffy, and disappeared into the device.

While this was happening, Mulder and Scully had been carefully positioning themselves to approach the specter from below, fervently trying to ignore the green goop on the ground, the goop that was all too familiar to them; and their nightmares.

After the eagle was channeled into the device, a gun shot rang through the air like a thunderclap, barely clipping the top of the ghost's hair and sending him head over heel through the air in a vain attempt to regain balance of the little mass he had.

The ghost looked on like a deer trapped in head lights at the ashy tip of his mop of hair. He floated still for several moments before turning toward the source of the blast-a red haired woman in a black trench coat, who was leveling the gun to once again be aimed at his head from behind a car.

He stared at her before yelling,"What, pray tell, was that about?! I didn't do anything to you, I was protecting the damn school from that eagle! Besides, you're plainly not the guys in white, or the Red Hunter, or the Fentons, so who are you, and _why, _exactly, _ARE YOU SHOOTING AT ME?!_"

His eyes caught those of the red headed figure, now accompanied by a tall brown haired man who was also in a black trench coat. Scully's face, at first, was one of shock upon hearing the infamous ghost speaking words to her, but soon her cool returned. She called back, "Stay where you are!"

The ghost peered at her patronizingly for a minute before retorting, "Why should I hang around someone shooting a gun at me? It doesn't really fit with my logic to stay within firing range of a couple of people trying to pump me full of lead. Not that it'd work, but still."

Mulder shook his head as he heard the ghost's comments, letting out a frustrated grunt as he sidestepped the stuff leaking out of Phantom's wound. It was getting harder and harder not to shudder as the disgusting substance dribbled off the 'ghost' . He turned back and joined in, yelling, "You have some explaining that needs to be done!"

The ghost grumbled, muttering, "I don't have time for this..." before once again becoming transparent and flying away, toward and above the school's roof. He made himself unable to be tracked by flying against the sun, where nothing could see him without blinding themselves.

Mulder and Scully lowered their guns, watching the figure disappear as best they could. They stared for a moment at the horizon before turning back to the crime scene. On the ground were several feathers and the green blood belonging to the ghost they were after, remnants of the battle.

"-and to think I hoped that would work for once." Mulder said, breaking the silence. His eyes scrunched and his shoulders tensed and fell in frustration, confusion and annoyance. So close, they'd gotten to damn close to finally catching one.

Scully dismissed her urge to agree, thinking of the specimens caked in green slime on the bacteria infested ground. She whipped out her cell phone and pressed her speed dial, saying into it, "Amity Police, this is Special Agent Dana Scully of the FBI. I have a crime scene I need fenced off in front of Casper High School. Bring evidence bags, stat."

She looked back toward the parking lot now adorned with glowing green bodily juices, slowly spreading across the concrete and dripping through the cracks, leaving a glowing trail wherever they touched.

XXX

Yellow tape was fencing off the scene. Scully was observing the evidence collecting while Mulder was telling the police a report of what happened. She took a small vile and, using a Q-tip, placed the feathers in a bag and a small amount of the ectoplasm in the vile, looking grimly at the skid mark covered concrete that was sure to have tampered with the samples. The joys of field work.

Mulder was looking rather perturbed while explaining to the police that a glowing eagle and Danny Phantom had attacked the school. They believed him, but were pestering for details he couldn't give, such as what direction the ghosts had come from and the like. Still, to their credit, they were treating it like any other crime, same questions- or maybe it was just desensitization.

Finally, they left him be to discuss plans of attack, leaving him to his own devices. He walked toward where Scully was kneeling on the ground, his dark frown equal to hers. He kneeled down to Scully's height, watching her open evidence bags and use tweezers to put them in.

"What do you think it is, Scully? As far as I know ghost's don't bleed. Walls bleed, floors bleed, _hybrids _bleed, but not ghosts." He asked, hoping she had a theory- because he sure didn't. At least, not until he let his memories start to take hold.

" ...Scully, what if he's a hybrid? I mean, look at it... Green blood, inhuman abilities, and more secretiveness than the lone gunmen put together. It all fits... But how could they really be back? We stopped them, after we escaped in the desert after my botched trial... Scully, you know as well as I do the steps we took." Mulder asked, eying the liquid.

Scully took a shaky breath before shrugging, shaking her head. "I don't know Mulder. I would first think a teenage prank, but there is no feasible way to make your blood green without doing you in. No _human _way, in any case. There was also no bulge where a flotation device could be hidden, either; he was really flying, Mulder." she murmured while moving some of the baggies containing various this and that into the bigger container.

"Unless either super heroes exist or there's a hybrid group we don't know about, there is no way for what that thing did to be possible. and I haven't seem superman around lately" she said as carefully positioning the evidence bags so as not to squish each other, and then standing to leave.

"I'm going to have these analyzed in the labs, we'll work from there. I'll check them out and compare them to other samples, see if there's any major differences to what we already have- including the blood of those infected with the black oil."

At the words, Mulder shook slightly, his imagination running away with him to old nightmares and frights. He shook himself free long enough to catch Scully's words,

"There is a small chance it has something like a genetic system, so we may be able to have some DNA tests run. Some samples from other ghosts have DNA similar to that the person had before death. We could get an identity... Hopefully. One about a quarter have it, but we can hope."

She took the samples and placed them in the backseat of her car. She gestured to Mulder, who rose and also took a seat and to leave with her to the hotel, where their laptops were waiting.

On the side lines of the school, the black haired boy, as well as a pale skinned, black haired girl and an African American boy were looking at the crime scene, flinching at the grizzly sight. They walked on before, once getting out of eye sight, running off and left, down a back street. However, the black haired boy slowed for a minute to rub his arm painfully, before catching up with the others.


End file.
